Starting phenix.real_space_refine on Sat May 2 12:00:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.map" model { file = "/net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vie_65085/05_2026/9vie_65085.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 26 5.16 5 C 3074 2.51 5 N 830 2.21 5 O 812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4746 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1109 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "B" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1174 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 0.77, per 1000 atoms: 0.16 Number of scatterers: 4746 At special positions: 0 Unit cell: (74.46, 82.62, 65.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 26 16.00 O 812 8.00 N 830 7.00 C 3074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 93.2 milliseconds 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 82.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 94 through 113 removed outlier: 4.245A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.584A pdb=" N ALA B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.025A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS B 44 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 72 Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 101 through 118 removed outlier: 4.168A pdb=" N LEU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 94 through 113 removed outlier: 4.245A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.584A pdb=" N ALA D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.025A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N HIS D 44 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 72 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 95 Processing helix chain 'D' and resid 101 through 118 removed outlier: 4.168A pdb=" N LEU D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 142 326 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 1870 1.38 - 1.57: 2972 1.57 - 1.75: 2 1.75 - 1.93: 38 1.93 - 2.12: 14 Bond restraints: 4896 Sorted by residual: bond pdb=" C CMO A 202 " pdb=" O CMO A 202 " ideal model delta sigma weight residual 1.141 1.286 -0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" C CMO C 202 " pdb=" O CMO C 202 " ideal model delta sigma weight residual 1.141 1.286 -0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" C CMO B 202 " pdb=" O CMO B 202 " ideal model delta sigma weight residual 1.141 1.271 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C CMO D 202 " pdb=" O CMO D 202 " ideal model delta sigma weight residual 1.141 1.271 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " ideal model delta sigma weight residual 1.544 1.431 0.113 2.00e-02 2.50e+03 3.22e+01 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5296 1.86 - 3.71: 1120 3.71 - 5.57: 202 5.57 - 7.43: 46 7.43 - 9.28: 6 Bond angle restraints: 6670 Sorted by residual: angle pdb=" CA ASP B 4 " pdb=" CB ASP B 4 " pdb=" CG ASP B 4 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA ASP D 4 " pdb=" CB ASP D 4 " pdb=" CG ASP D 4 " ideal model delta sigma weight residual 112.60 118.94 -6.34 1.00e+00 1.00e+00 4.02e+01 angle pdb=" CA HIS C 87 " pdb=" CB HIS C 87 " pdb=" CG HIS C 87 " ideal model delta sigma weight residual 113.80 107.83 5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA HIS A 87 " pdb=" CB HIS A 87 " pdb=" CG HIS A 87 " ideal model delta sigma weight residual 113.80 107.83 5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA ASP D 19 " pdb=" CB ASP D 19 " pdb=" CG ASP D 19 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 ... (remaining 6665 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.93: 2512 17.93 - 35.85: 210 35.85 - 53.78: 40 53.78 - 71.70: 22 71.70 - 89.62: 18 Dihedral angle restraints: 2802 sinusoidal: 1114 harmonic: 1688 Sorted by residual: dihedral pdb=" CD ARG A 92 " pdb=" NE ARG A 92 " pdb=" CZ ARG A 92 " pdb=" NH1 ARG A 92 " ideal model delta sinusoidal sigma weight residual 0.00 -33.09 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CD ARG C 92 " pdb=" NE ARG C 92 " pdb=" CZ ARG C 92 " pdb=" NH1 ARG C 92 " ideal model delta sinusoidal sigma weight residual 0.00 -33.09 33.09 1 1.00e+01 1.00e-02 1.56e+01 dihedral pdb=" CA THR C 137 " pdb=" C THR C 137 " pdb=" N SER C 138 " pdb=" CA SER C 138 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 2799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 350 0.055 - 0.110: 196 0.110 - 0.165: 86 0.165 - 0.219: 42 0.219 - 0.274: 12 Chirality restraints: 686 Sorted by residual: chirality pdb=" CA PRO D 100 " pdb=" N PRO D 100 " pdb=" C PRO D 100 " pdb=" CB PRO D 100 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PRO B 100 " pdb=" N PRO B 100 " pdb=" C PRO B 100 " pdb=" CB PRO B 100 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 73 " pdb=" CA ILE A 73 " pdb=" CG1 ILE A 73 " pdb=" CG2 ILE A 73 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 683 not shown) Planarity restraints: 836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 14 " 0.118 2.00e-02 2.50e+03 5.59e-02 7.82e+01 pdb=" CG TRP A 14 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 14 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 14 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP A 14 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 14 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 14 " -0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 14 " 0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 14 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 14 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 14 " -0.118 2.00e-02 2.50e+03 5.59e-02 7.82e+01 pdb=" CG TRP C 14 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 14 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP C 14 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP C 14 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 14 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP C 14 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 14 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 14 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP C 14 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 41 " 0.099 2.00e-02 2.50e+03 5.12e-02 5.23e+01 pdb=" CG TYR D 41 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR D 41 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR D 41 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR D 41 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR D 41 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 41 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 41 " 0.061 2.00e-02 2.50e+03 ... (remaining 833 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 650 2.78 - 3.31: 4578 3.31 - 3.84: 8124 3.84 - 4.37: 10554 4.37 - 4.90: 16484 Nonbonded interactions: 40390 Sorted by model distance: nonbonded pdb=" OD2 ASP B 99 " pdb=" OH TYR C 42 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 42 " pdb=" OD2 ASP D 99 " model vdw 2.252 3.040 nonbonded pdb="FE HEM C 201 " pdb=" C CMO C 202 " model vdw 2.336 3.230 nonbonded pdb="FE HEM A 201 " pdb=" C CMO A 202 " model vdw 2.336 3.230 nonbonded pdb=" OG SER B 89 " pdb=" O LEU B 141 " model vdw 2.463 3.040 ... (remaining 40385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.530 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.205 4900 Z= 0.785 Angle : 1.635 9.283 6670 Z= 1.068 Chirality : 0.089 0.274 686 Planarity : 0.022 0.285 836 Dihedral : 16.944 89.625 1698 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.92 % Allowed : 2.08 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.31), residues: 566 helix: -1.33 (0.21), residues: 416 sheet: None (None), residues: 0 loop : 0.48 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.008 ARG B 40 TYR 0.099 0.015 TYR D 41 PHE 0.043 0.011 PHE B 130 TRP 0.118 0.024 TRP A 14 HIS 0.020 0.005 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.01424 ( 4896) covalent geometry : angle 1.63542 ( 6670) hydrogen bonds : bond 0.22591 ( 326) hydrogen bonds : angle 6.72029 ( 906) Misc. bond : bond 0.14901 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.096 Fit side-chains REVERT: A 4 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6866 (mmp) REVERT: A 5 GLU cc_start: 0.7008 (tp30) cc_final: 0.6103 (tm-30) REVERT: A 11 LYS cc_start: 0.7669 (mttt) cc_final: 0.7294 (mttp) REVERT: A 92 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6977 (mmt180) REVERT: A 99 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7859 (mtmt) REVERT: A 120 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6948 (mp0) REVERT: B 13 ASP cc_start: 0.8461 (m-30) cc_final: 0.8232 (m-30) REVERT: B 40 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6319 (ptm160) REVERT: B 59 LYS cc_start: 0.7882 (mttt) cc_final: 0.7463 (mtpt) REVERT: B 76 LYS cc_start: 0.7623 (mtpt) cc_final: 0.7090 (mptp) REVERT: B 94 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7931 (mt-10) REVERT: B 101 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 104 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7419 (mtmm) REVERT: B 120 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6975 (mp0) REVERT: B 125 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7176 (mp0) REVERT: C 4 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.6864 (mmp) REVERT: C 5 GLU cc_start: 0.7004 (tp30) cc_final: 0.6099 (tm-30) REVERT: C 11 LYS cc_start: 0.7667 (mttt) cc_final: 0.7293 (mttp) REVERT: C 92 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6976 (mmt180) REVERT: C 99 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7860 (mtmt) REVERT: C 120 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6947 (mp0) REVERT: D 13 ASP cc_start: 0.8460 (m-30) cc_final: 0.8232 (m-30) REVERT: D 40 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6317 (ptm160) REVERT: D 59 LYS cc_start: 0.7883 (mttt) cc_final: 0.7464 (mtpt) REVERT: D 76 LYS cc_start: 0.7624 (mtpt) cc_final: 0.7090 (mptp) REVERT: D 94 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 101 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8229 (mm-30) REVERT: D 104 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7419 (mtmm) REVERT: D 120 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6977 (mp0) REVERT: D 125 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7178 (mp0) outliers start: 14 outliers final: 2 residues processed: 124 average time/residue: 0.5209 time to fit residues: 66.1041 Evaluate side-chains 110 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 40 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS B 87 ASN B 102 ASN C 50 HIS D 52 HIS D 87 ASN D 102 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117642 restraints weight = 4005.136| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.41 r_work: 0.3131 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4900 Z= 0.125 Angle : 0.570 5.472 6670 Z= 0.281 Chirality : 0.040 0.129 686 Planarity : 0.004 0.043 836 Dihedral : 11.768 82.858 664 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.88 % Allowed : 6.88 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.34), residues: 566 helix: 1.48 (0.24), residues: 412 sheet: None (None), residues: 0 loop : 1.17 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 92 TYR 0.011 0.001 TYR B 41 PHE 0.013 0.001 PHE D 130 TRP 0.013 0.002 TRP A 14 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4896) covalent geometry : angle 0.56982 ( 6670) hydrogen bonds : bond 0.04203 ( 326) hydrogen bonds : angle 4.08255 ( 906) Misc. bond : bond 0.05571 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.102 Fit side-chains REVERT: A 11 LYS cc_start: 0.7855 (mttt) cc_final: 0.7416 (mttp) REVERT: A 85 GLU cc_start: 0.6537 (pt0) cc_final: 0.5793 (pp20) REVERT: A 99 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8082 (mtmt) REVERT: A 127 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7923 (mtmm) REVERT: B 6 HIS cc_start: 0.7836 (m170) cc_final: 0.7457 (m-70) REVERT: B 13 ASP cc_start: 0.8750 (m-30) cc_final: 0.8385 (m-30) REVERT: B 59 LYS cc_start: 0.8178 (mttt) cc_final: 0.7751 (mtpt) REVERT: B 62 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7792 (mm-30) REVERT: B 76 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7473 (mptp) REVERT: B 120 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7383 (mp0) REVERT: B 125 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7838 (mp0) REVERT: C 11 LYS cc_start: 0.7851 (mttt) cc_final: 0.7406 (mttp) REVERT: C 85 GLU cc_start: 0.6531 (pt0) cc_final: 0.5781 (pp20) REVERT: C 99 LYS cc_start: 0.8386 (mtmt) cc_final: 0.8094 (mtmt) REVERT: C 120 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7248 (mp0) REVERT: C 127 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7919 (mtmm) REVERT: D 6 HIS cc_start: 0.7843 (m170) cc_final: 0.7463 (m-70) REVERT: D 13 ASP cc_start: 0.8752 (m-30) cc_final: 0.8388 (m-30) REVERT: D 59 LYS cc_start: 0.8173 (mttt) cc_final: 0.7747 (mtpt) REVERT: D 62 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7790 (mm-30) REVERT: D 76 LYS cc_start: 0.7813 (mtpt) cc_final: 0.7480 (mptp) REVERT: D 120 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7396 (mp0) REVERT: D 125 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7854 (mp0) outliers start: 9 outliers final: 2 residues processed: 113 average time/residue: 0.4837 time to fit residues: 56.0848 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain C residue 61 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 56 HIS B 61 GLN B 87 ASN B 117 HIS C 71 ASN D 56 HIS D 61 GLN D 87 ASN D 117 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.142071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.117910 restraints weight = 4000.159| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.37 r_work: 0.3133 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 4900 Z= 0.123 Angle : 0.553 5.317 6670 Z= 0.267 Chirality : 0.039 0.122 686 Planarity : 0.004 0.047 836 Dihedral : 9.656 84.257 640 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.25 % Allowed : 11.88 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.35), residues: 566 helix: 2.08 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.26 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 31 TYR 0.011 0.002 TYR D 41 PHE 0.010 0.001 PHE C 63 TRP 0.011 0.002 TRP C 14 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4896) covalent geometry : angle 0.55286 ( 6670) hydrogen bonds : bond 0.04234 ( 326) hydrogen bonds : angle 3.95443 ( 906) Misc. bond : bond 0.08008 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.096 Fit side-chains REVERT: A 11 LYS cc_start: 0.7816 (mttt) cc_final: 0.7456 (mttp) REVERT: A 51 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7714 (m110) REVERT: A 85 GLU cc_start: 0.6545 (pt0) cc_final: 0.5815 (pp20) REVERT: A 99 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8129 (mtmt) REVERT: B 6 HIS cc_start: 0.7829 (m170) cc_final: 0.7526 (m-70) REVERT: B 59 LYS cc_start: 0.8141 (mttt) cc_final: 0.7780 (mtpt) REVERT: B 61 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7397 (mp10) REVERT: B 62 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7812 (mm-30) REVERT: B 76 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7556 (mmtm) REVERT: B 90 LYS cc_start: 0.7949 (pttp) cc_final: 0.7622 (pptt) REVERT: B 120 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7376 (mp0) REVERT: B 125 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7949 (mp0) REVERT: C 11 LYS cc_start: 0.7804 (mttt) cc_final: 0.7441 (mttp) REVERT: C 85 GLU cc_start: 0.6553 (pt0) cc_final: 0.5816 (pp20) REVERT: C 99 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8143 (mtmt) REVERT: C 120 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7273 (mp0) REVERT: D 6 HIS cc_start: 0.7815 (m170) cc_final: 0.7510 (m-70) REVERT: D 59 LYS cc_start: 0.8150 (mttt) cc_final: 0.7791 (mtpt) REVERT: D 61 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7416 (mp10) REVERT: D 76 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7556 (mmtm) REVERT: D 90 LYS cc_start: 0.7941 (pttp) cc_final: 0.7617 (pptt) REVERT: D 120 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7388 (mp0) REVERT: D 125 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7945 (mp0) outliers start: 6 outliers final: 2 residues processed: 102 average time/residue: 0.4886 time to fit residues: 51.1258 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain C residue 81 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.141299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117345 restraints weight = 3999.643| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.35 r_work: 0.3128 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 4900 Z= 0.133 Angle : 0.562 5.402 6670 Z= 0.273 Chirality : 0.040 0.122 686 Planarity : 0.004 0.050 836 Dihedral : 9.267 82.061 640 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.46 % Allowed : 12.29 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.36), residues: 566 helix: 2.19 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.29 (0.56), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.011 0.002 TYR B 41 PHE 0.008 0.001 PHE C 63 TRP 0.011 0.002 TRP C 14 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4896) covalent geometry : angle 0.56206 ( 6670) hydrogen bonds : bond 0.04411 ( 326) hydrogen bonds : angle 3.96937 ( 906) Misc. bond : bond 0.08642 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.097 Fit side-chains REVERT: A 4 MET cc_start: 0.7399 (mmm) cc_final: 0.6822 (mmp) REVERT: A 5 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6230 (tm-30) REVERT: A 11 LYS cc_start: 0.7808 (mttt) cc_final: 0.7423 (mttp) REVERT: A 85 GLU cc_start: 0.6532 (pt0) cc_final: 0.5793 (pp20) REVERT: A 99 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8144 (mtmt) REVERT: A 127 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7751 (mtmm) REVERT: B 6 HIS cc_start: 0.7852 (m170) cc_final: 0.7523 (m-70) REVERT: B 8 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7421 (mtt-85) REVERT: B 59 LYS cc_start: 0.8165 (mttt) cc_final: 0.7790 (mtpt) REVERT: B 61 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7448 (mp10) REVERT: B 62 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 76 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7570 (mmtm) REVERT: B 90 LYS cc_start: 0.7980 (pttp) cc_final: 0.7646 (pptt) REVERT: B 120 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7399 (mp0) REVERT: B 125 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7927 (mp0) REVERT: C 4 MET cc_start: 0.7380 (mmm) cc_final: 0.6802 (mmp) REVERT: C 5 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: C 11 LYS cc_start: 0.7798 (mttt) cc_final: 0.7409 (mttp) REVERT: C 85 GLU cc_start: 0.6535 (pt0) cc_final: 0.5791 (pp20) REVERT: C 99 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8151 (mtmt) REVERT: C 120 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7257 (mp0) REVERT: C 127 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7736 (mtmm) REVERT: D 6 HIS cc_start: 0.7843 (m170) cc_final: 0.7512 (m-70) REVERT: D 8 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7418 (mtt-85) REVERT: D 59 LYS cc_start: 0.8166 (mttt) cc_final: 0.7795 (mtpt) REVERT: D 61 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7448 (mp10) REVERT: D 76 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7567 (mmtm) REVERT: D 90 LYS cc_start: 0.7971 (pttp) cc_final: 0.7641 (pptt) REVERT: D 120 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7414 (mp0) REVERT: D 125 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7939 (mp0) outliers start: 7 outliers final: 2 residues processed: 101 average time/residue: 0.4929 time to fit residues: 51.0538 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 81 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117757 restraints weight = 4027.838| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.38 r_work: 0.3134 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 4900 Z= 0.127 Angle : 0.550 5.380 6670 Z= 0.265 Chirality : 0.040 0.118 686 Planarity : 0.004 0.050 836 Dihedral : 9.301 82.515 640 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.04 % Allowed : 12.71 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.36), residues: 566 helix: 2.27 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.41 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.010 0.001 TYR D 41 PHE 0.008 0.001 PHE A 63 TRP 0.010 0.002 TRP A 14 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4896) covalent geometry : angle 0.54957 ( 6670) hydrogen bonds : bond 0.04198 ( 326) hydrogen bonds : angle 3.92754 ( 906) Misc. bond : bond 0.08581 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.097 Fit side-chains REVERT: A 11 LYS cc_start: 0.7767 (mttt) cc_final: 0.7375 (mttp) REVERT: A 85 GLU cc_start: 0.6543 (pt0) cc_final: 0.5792 (pp20) REVERT: A 99 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8094 (mtmt) REVERT: A 127 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7789 (mtmm) REVERT: B 6 HIS cc_start: 0.7831 (m170) cc_final: 0.7508 (m-70) REVERT: B 8 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7386 (mtt-85) REVERT: B 59 LYS cc_start: 0.8127 (mttt) cc_final: 0.7750 (mtpt) REVERT: B 61 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7373 (mp10) REVERT: B 62 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7780 (mm-30) REVERT: B 76 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7547 (mmtm) REVERT: B 90 LYS cc_start: 0.7954 (pttp) cc_final: 0.7583 (pptt) REVERT: B 120 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7348 (mp0) REVERT: B 125 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7810 (mp0) REVERT: C 11 LYS cc_start: 0.7760 (mttt) cc_final: 0.7367 (mttp) REVERT: C 85 GLU cc_start: 0.6542 (pt0) cc_final: 0.5791 (pp20) REVERT: C 99 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8104 (mtmt) REVERT: C 120 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7208 (mp0) REVERT: C 127 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7798 (mtmm) REVERT: D 6 HIS cc_start: 0.7827 (m170) cc_final: 0.7499 (m-70) REVERT: D 8 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7382 (mtt-85) REVERT: D 59 LYS cc_start: 0.8132 (mttt) cc_final: 0.7761 (mtpt) REVERT: D 61 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7397 (mp10) REVERT: D 76 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7539 (mmtm) REVERT: D 90 LYS cc_start: 0.7950 (pttp) cc_final: 0.7582 (pptt) REVERT: D 120 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7361 (mp0) REVERT: D 125 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7815 (mp0) outliers start: 5 outliers final: 2 residues processed: 99 average time/residue: 0.5001 time to fit residues: 50.7616 Evaluate side-chains 98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain C residue 81 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.0040 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.140326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116285 restraints weight = 4047.690| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.36 r_work: 0.3115 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 4900 Z= 0.159 Angle : 0.593 5.500 6670 Z= 0.290 Chirality : 0.043 0.123 686 Planarity : 0.005 0.051 836 Dihedral : 9.399 82.023 640 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.67 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.36), residues: 566 helix: 2.12 (0.25), residues: 410 sheet: None (None), residues: 0 loop : 1.32 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.013 0.002 TYR D 41 PHE 0.008 0.002 PHE C 43 TRP 0.011 0.003 TRP C 14 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4896) covalent geometry : angle 0.59273 ( 6670) hydrogen bonds : bond 0.04952 ( 326) hydrogen bonds : angle 4.02941 ( 906) Misc. bond : bond 0.09760 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.094 Fit side-chains REVERT: A 11 LYS cc_start: 0.7861 (mttt) cc_final: 0.7462 (mttp) REVERT: A 85 GLU cc_start: 0.6571 (pt0) cc_final: 0.5831 (pp20) REVERT: A 99 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8175 (mtmt) REVERT: A 127 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7868 (mtmm) REVERT: B 6 HIS cc_start: 0.7912 (m170) cc_final: 0.7568 (m-70) REVERT: B 8 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7412 (mtt-85) REVERT: B 59 LYS cc_start: 0.8259 (mttt) cc_final: 0.7843 (mtpt) REVERT: B 76 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7622 (mmtm) REVERT: B 90 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7677 (pptt) REVERT: B 120 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7433 (mp0) REVERT: B 125 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7662 (mp0) REVERT: C 11 LYS cc_start: 0.7836 (mttt) cc_final: 0.7433 (mttp) REVERT: C 85 GLU cc_start: 0.6573 (pt0) cc_final: 0.5831 (pp20) REVERT: C 99 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8183 (mtmt) REVERT: C 120 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7301 (mp0) REVERT: C 127 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7854 (mtmm) REVERT: D 6 HIS cc_start: 0.7910 (m170) cc_final: 0.7566 (m-70) REVERT: D 8 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7413 (mtt-85) REVERT: D 59 LYS cc_start: 0.8245 (mttt) cc_final: 0.7832 (mtpt) REVERT: D 62 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7651 (mm-30) REVERT: D 76 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7624 (mmtm) REVERT: D 90 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7676 (pptt) REVERT: D 120 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7453 (mp0) REVERT: D 125 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7655 (mp0) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 0.4780 time to fit residues: 50.0282 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain D residue 90 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.142396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118253 restraints weight = 3981.553| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.38 r_work: 0.3140 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 4900 Z= 0.124 Angle : 0.547 5.296 6670 Z= 0.263 Chirality : 0.039 0.117 686 Planarity : 0.004 0.051 836 Dihedral : 9.313 82.676 640 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.25 % Allowed : 12.71 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.36), residues: 566 helix: 2.27 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.44 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 31 TYR 0.009 0.001 TYR D 41 PHE 0.008 0.001 PHE D 130 TRP 0.010 0.002 TRP A 14 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4896) covalent geometry : angle 0.54684 ( 6670) hydrogen bonds : bond 0.04106 ( 326) hydrogen bonds : angle 3.96081 ( 906) Misc. bond : bond 0.08464 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.096 Fit side-chains REVERT: A 11 LYS cc_start: 0.7713 (mttt) cc_final: 0.7316 (mttp) REVERT: A 85 GLU cc_start: 0.6468 (pt0) cc_final: 0.5749 (pp20) REVERT: A 99 LYS cc_start: 0.8411 (mtmt) cc_final: 0.8098 (mtmt) REVERT: A 127 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7808 (mtmm) REVERT: B 6 HIS cc_start: 0.7843 (m170) cc_final: 0.7501 (m-70) REVERT: B 8 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7414 (mtt-85) REVERT: B 59 LYS cc_start: 0.8092 (mttt) cc_final: 0.7717 (mtpt) REVERT: B 76 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7567 (mmtm) REVERT: B 90 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7576 (pptt) REVERT: B 120 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7353 (mp0) REVERT: B 125 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7502 (mp0) REVERT: C 5 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6154 (tm-30) REVERT: C 11 LYS cc_start: 0.7698 (mttt) cc_final: 0.7297 (mttp) REVERT: C 85 GLU cc_start: 0.6477 (pt0) cc_final: 0.5760 (pp20) REVERT: C 99 LYS cc_start: 0.8420 (mtmt) cc_final: 0.8107 (mtmt) REVERT: C 120 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7231 (mp0) REVERT: C 127 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7795 (mtmm) REVERT: D 6 HIS cc_start: 0.7835 (m170) cc_final: 0.7493 (m-70) REVERT: D 8 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7410 (mtt-85) REVERT: D 59 LYS cc_start: 0.8037 (mttt) cc_final: 0.7652 (mtpt) REVERT: D 76 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7559 (mmtm) REVERT: D 90 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7570 (pptt) REVERT: D 120 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7365 (mp0) REVERT: D 125 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7499 (mp0) outliers start: 6 outliers final: 3 residues processed: 96 average time/residue: 0.5110 time to fit residues: 50.3182 Evaluate side-chains 100 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain D residue 90 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118523 restraints weight = 4045.899| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.39 r_work: 0.3144 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 4900 Z= 0.121 Angle : 0.542 5.348 6670 Z= 0.259 Chirality : 0.039 0.115 686 Planarity : 0.004 0.050 836 Dihedral : 9.288 82.769 640 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.46 % Allowed : 12.71 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.36), residues: 566 helix: 2.33 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.44 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.009 0.001 TYR B 41 PHE 0.008 0.001 PHE A 63 TRP 0.010 0.002 TRP C 14 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4896) covalent geometry : angle 0.54173 ( 6670) hydrogen bonds : bond 0.04013 ( 326) hydrogen bonds : angle 3.93389 ( 906) Misc. bond : bond 0.08652 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.108 Fit side-chains REVERT: A 11 LYS cc_start: 0.7708 (mttt) cc_final: 0.7325 (mttp) REVERT: A 85 GLU cc_start: 0.6515 (pt0) cc_final: 0.5770 (pp20) REVERT: A 99 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8085 (mtmt) REVERT: A 115 SER cc_start: 0.8334 (p) cc_final: 0.8095 (m) REVERT: A 127 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7786 (mtmm) REVERT: B 6 HIS cc_start: 0.7801 (m170) cc_final: 0.7480 (m-70) REVERT: B 8 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7378 (mtt-85) REVERT: B 59 LYS cc_start: 0.8101 (mttt) cc_final: 0.7727 (mtpt) REVERT: B 76 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7568 (mmtm) REVERT: B 90 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7555 (pptt) REVERT: B 120 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7349 (mp0) REVERT: B 125 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7491 (mp0) REVERT: C 5 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6146 (tm-30) REVERT: C 11 LYS cc_start: 0.7691 (mttt) cc_final: 0.7306 (mttp) REVERT: C 85 GLU cc_start: 0.6521 (pt0) cc_final: 0.5774 (pp20) REVERT: C 99 LYS cc_start: 0.8410 (mtmt) cc_final: 0.8094 (mtmt) REVERT: C 115 SER cc_start: 0.8347 (p) cc_final: 0.8111 (m) REVERT: C 120 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7211 (mp0) REVERT: C 127 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7780 (mtmm) REVERT: D 6 HIS cc_start: 0.7798 (m170) cc_final: 0.7475 (m-70) REVERT: D 8 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7376 (mtt-85) REVERT: D 59 LYS cc_start: 0.8085 (mttt) cc_final: 0.7709 (mtpt) REVERT: D 62 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7615 (mm-30) REVERT: D 76 LYS cc_start: 0.7793 (mtpt) cc_final: 0.7555 (mmtm) REVERT: D 90 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7555 (pptt) REVERT: D 120 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7360 (mp0) REVERT: D 125 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7489 (mp0) outliers start: 7 outliers final: 3 residues processed: 99 average time/residue: 0.4936 time to fit residues: 50.1338 Evaluate side-chains 102 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain D residue 90 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 87 ASN C 71 ASN D 61 GLN D 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118083 restraints weight = 4001.925| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.38 r_work: 0.3138 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 4900 Z= 0.129 Angle : 0.555 5.388 6670 Z= 0.266 Chirality : 0.040 0.117 686 Planarity : 0.004 0.050 836 Dihedral : 9.308 82.503 640 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.46 % Allowed : 12.92 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.36), residues: 566 helix: 2.30 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.39 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.010 0.001 TYR B 41 PHE 0.008 0.001 PHE A 63 TRP 0.011 0.002 TRP A 14 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 4896) covalent geometry : angle 0.55508 ( 6670) hydrogen bonds : bond 0.04220 ( 326) hydrogen bonds : angle 3.94423 ( 906) Misc. bond : bond 0.08874 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.098 Fit side-chains REVERT: A 11 LYS cc_start: 0.7720 (mttt) cc_final: 0.7331 (mttp) REVERT: A 85 GLU cc_start: 0.6468 (pt0) cc_final: 0.5750 (pp20) REVERT: A 99 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8106 (mtmt) REVERT: A 127 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7803 (mtmm) REVERT: B 6 HIS cc_start: 0.7883 (m170) cc_final: 0.7517 (m-70) REVERT: B 8 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7383 (mtt-85) REVERT: B 59 LYS cc_start: 0.8124 (mttt) cc_final: 0.7748 (mtpt) REVERT: B 76 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7583 (mmtm) REVERT: B 90 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7583 (pptt) REVERT: B 120 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7360 (mp0) REVERT: B 125 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7512 (mp0) REVERT: C 5 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6158 (tm-30) REVERT: C 11 LYS cc_start: 0.7706 (mttt) cc_final: 0.7316 (mttp) REVERT: C 85 GLU cc_start: 0.6468 (pt0) cc_final: 0.5750 (pp20) REVERT: C 99 LYS cc_start: 0.8423 (mtmt) cc_final: 0.8111 (mtmt) REVERT: C 120 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7233 (mp0) REVERT: C 127 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7788 (mtmm) REVERT: D 6 HIS cc_start: 0.7881 (m170) cc_final: 0.7512 (m-70) REVERT: D 8 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7383 (mtt-85) REVERT: D 59 LYS cc_start: 0.8104 (mttt) cc_final: 0.7724 (mtpt) REVERT: D 76 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7575 (mmtm) REVERT: D 90 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7584 (pptt) REVERT: D 120 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7379 (mp0) REVERT: D 125 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7509 (mp0) outliers start: 7 outliers final: 2 residues processed: 97 average time/residue: 0.5064 time to fit residues: 50.3583 Evaluate side-chains 99 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain C residue 81 CYS Chi-restraints excluded: chain D residue 90 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 71 ASN B 87 ASN C 71 ASN D 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121314 restraints weight = 3978.417| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.39 r_work: 0.3177 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4900 Z= 0.103 Angle : 0.521 5.134 6670 Z= 0.243 Chirality : 0.037 0.110 686 Planarity : 0.004 0.050 836 Dihedral : 9.169 83.202 640 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.83 % Allowed : 13.54 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.36), residues: 566 helix: 2.54 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.46 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.007 0.001 TYR B 41 PHE 0.009 0.001 PHE C 63 TRP 0.009 0.002 TRP A 14 HIS 0.004 0.001 HIS D 127 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4896) covalent geometry : angle 0.52112 ( 6670) hydrogen bonds : bond 0.03346 ( 326) hydrogen bonds : angle 3.82423 ( 906) Misc. bond : bond 0.06684 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.098 Fit side-chains REVERT: A 11 LYS cc_start: 0.7724 (mttt) cc_final: 0.7256 (mttp) REVERT: A 85 GLU cc_start: 0.6572 (pt0) cc_final: 0.5832 (pp20) REVERT: A 99 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8066 (mtmt) REVERT: A 127 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7757 (mtmm) REVERT: B 6 HIS cc_start: 0.7770 (m170) cc_final: 0.7401 (m-70) REVERT: B 8 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7396 (mtt-85) REVERT: B 59 LYS cc_start: 0.8099 (mttt) cc_final: 0.7722 (mtpt) REVERT: B 76 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7563 (mmtm) REVERT: B 90 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7670 (pptt) REVERT: B 120 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7319 (mp0) REVERT: B 125 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7525 (mp0) REVERT: C 5 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6258 (tm-30) REVERT: C 11 LYS cc_start: 0.7707 (mttt) cc_final: 0.7231 (mttp) REVERT: C 85 GLU cc_start: 0.6567 (pt0) cc_final: 0.5803 (pp20) REVERT: C 99 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8078 (mtmt) REVERT: C 115 SER cc_start: 0.8321 (p) cc_final: 0.8116 (m) REVERT: C 120 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7250 (mp0) REVERT: C 127 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7730 (mtmm) REVERT: D 6 HIS cc_start: 0.7775 (m170) cc_final: 0.7400 (m-70) REVERT: D 8 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7394 (mtt-85) REVERT: D 59 LYS cc_start: 0.8070 (mttt) cc_final: 0.7693 (mtpt) REVERT: D 76 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7553 (mmtm) REVERT: D 90 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7663 (pptt) REVERT: D 120 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7330 (mp0) REVERT: D 125 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7524 (mp0) outliers start: 4 outliers final: 0 residues processed: 100 average time/residue: 0.5140 time to fit residues: 52.7257 Evaluate side-chains 101 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain C residue 5 GLU Chi-restraints excluded: chain D residue 90 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.0670 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 71 ASN B 87 ASN C 67 HIS C 71 ASN D 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121306 restraints weight = 4021.919| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.39 r_work: 0.3177 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 4900 Z= 0.103 Angle : 0.519 5.194 6670 Z= 0.243 Chirality : 0.037 0.109 686 Planarity : 0.004 0.049 836 Dihedral : 9.114 83.129 640 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.83 % Allowed : 12.92 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.36), residues: 566 helix: 2.61 (0.25), residues: 412 sheet: None (None), residues: 0 loop : 1.47 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 31 TYR 0.007 0.001 TYR D 41 PHE 0.009 0.001 PHE C 63 TRP 0.009 0.002 TRP A 14 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 4896) covalent geometry : angle 0.51907 ( 6670) hydrogen bonds : bond 0.03369 ( 326) hydrogen bonds : angle 3.79024 ( 906) Misc. bond : bond 0.06981 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1356.54 seconds wall clock time: 25 minutes 22.45 seconds (1522.45 seconds total)